Fine Structures of Intrinsically Disordered Proteins

We report simulation studies of about 40 intrinsically disordered proteins (IDPs) utilizing a coarse-grained bead-spring model where the interactions among amino acids are introduced through a hydropathy matrix and screened Coulomb interactions for charged amino acids. We examined two hydropathy scales, HPS1 and HPS2, and compared our findings with the experimental data. Our analysis revealed optimal interaction parameters of 0.1 kCal/mol for HPS1 and 0.2 kCal/mol for HPS2. Using these optimum parameters, we explored the universal scaling properties of the end-to-end distance and transverse fluctuation of the IDPs as well as sequence-specific properties of the IDPs. We introduced the Wilson charge index to capture charge interactions and their distribution in the sequence space and a skewness parameter to monitor the change in the gyration radii distribution with charge patches and charge asymmetry. Moreover, we study the variation of the radius of gyration as a function of salt concentration and classify the IDPs using their net and absolute charge content. These metrics unveil the finer characteristics of IDPs and contribute to a deeper understanding of IDPs, shedding light on their unique properties and the role they might play in biological processes and the emergence of life.